Skip Navigation


Bioinformatics Advance Access originally published online on June 5, 2007
Bioinformatics 2007 23(16):2031-2037; doi:10.1093/bioinformatics/btm299
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
23/16/2031    most recent
btm299v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Wong, W. S.W.
Right arrow Articles by Nielsen, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wong, W. S.W.
Right arrow Articles by Nielsen, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models

Wendy S.W. Wong 1,3,* and Rasmus Nielsen 2

1Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA, 2Department of Biology and Center for Comparative Genomics, University of Copenhagen, Universitetsparken 15, 2100 Kbh Ø, Denmark and 3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: Finding the regulatory modules for transcription factors binding is an important step in elucidating the complex molecular mechanisms underlying regulation of gene expression. There are numerous methods available for solving this problem, however, very few of them take advantage of the increasing availability of comparative genomic data.

Results: We develop a method for finding regulatory modules in Eukaryotic species using phylogenetic data. Using computer simulations and analysis of real data, we show that the use of phylogenetic hidden Markov model can lead to an increase in accuracy of prediction over methods that do not take advantage of the data from multiple species.

Availability: The new method is made accessible under GPL in a new publicly available JAVA program: EvoPromoter. It can be downloaded at http://sourceforge.net/projects/evopromoter/

Contact: sww8{at}cornell.edu

Associate Editor: Alex Bateman

Received on November 1, 2006; revised on May 28, 2007; accepted on May 29, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.